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- EMDB-64813: Phycobilisome rod R2 from Gloeobacter violaceus PCC 7421 -

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Basic information

Entry
Database: EMDB / ID: EMD-64813
TitlePhycobilisome rod R2 from Gloeobacter violaceus PCC 7421
Map data
Sample
  • Complex: Bundle-shaped phycobilisome
    • Protein or peptide: Phycocyanin-associated rod linker protein
    • Protein or peptide: Phycocyanin beta chain
    • Protein or peptide: Phycocyanin alpha chain
    • Protein or peptide: Phycocyanin-associated rod linker protein
    • Protein or peptide: Glr1262 protein
  • Ligand: PHYCOCYANOBILIN
KeywordsPhycobilisome / PHOTOSYNTHESIS
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
Phycocyanin beta chain / Phycocyanin alpha chain / Glr1262 protein
Similarity search - Component
Biological speciesGloeobacter violaceus PCC 7421 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsBurtseva AD / Baymukhametov TN / Slonimskiy YB / Popov VO / Sluchanko NN / Boyko KM
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Russian Science Foundation23-74-00062 Russian Federation
CitationJournal: Sci Adv / Year: 2025
Title: Structure and quenching of a bundle-shaped phycobilisome.
Authors: Anna D Burtseva / Yury B Slonimskiy / Timur N Baymukhametov / Maria A Sinetova / Daniil A Gvozdev / Georgy V Tsoraev / Dmitry A Cherepanov / Eugene G Maksimov / Vladimir O Popov / Konstantin ...Authors: Anna D Burtseva / Yury B Slonimskiy / Timur N Baymukhametov / Maria A Sinetova / Daniil A Gvozdev / Georgy V Tsoraev / Dmitry A Cherepanov / Eugene G Maksimov / Vladimir O Popov / Konstantin M Boyko / Nikolai N Sluchanko /
Abstract: Cyanobacteria use soluble antenna megacomplexes, phycobilisomes (PBSs), to maximize light-harvesting efficiency and small photoswitchable orange carotenoid proteins (OCPs) to down-regulate PBSs in ...Cyanobacteria use soluble antenna megacomplexes, phycobilisomes (PBSs), to maximize light-harvesting efficiency and small photoswitchable orange carotenoid proteins (OCPs) to down-regulate PBSs in high light. Among known PBS morphologies, the one from the basal cyanobacterial genus still lacks detailed structural characterization. Here, we reconstructed a cryo-electron microscopy structure of the >10-megadalton PBS, with diverging, conformationally mobile bundles of rods composed of stacked phycoerythrin and phycocyanin hexamers, stemming from a pentacylindrical allophycocyanin core belted by auxiliary phycocyanin hexamers. We show how two -specific multidomain linker proteins, Glr1262 and Glr2806, maintain this bundle-shaped architecture and reveal its differential regulation via nonphotochemical quenching by two OCP types of that recognize separate binding sites within the allophycocyanin core, including lateral cylinders absent in tricylindrical cores.
History
DepositionMay 28, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64813.png

Downloads & links

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Map

FileDownload / File: emd_64813.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 672 pix.
= 840. Å		1.25 Å/pix.
x 672 pix.
= 840. Å		1.25 Å/pix.
x 672 pix.
= 840. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.51879346 - 1.6434785
Average (Standard dev.)0.0021711057 (±0.03938034)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions672672672
Spacing672672672
CellA=B=C: 840.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64813_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64813_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bundle-shaped phycobilisome

EntireName: Bundle-shaped phycobilisome
Components
  • Complex: Bundle-shaped phycobilisome
    • Protein or peptide: Phycocyanin-associated rod linker protein
    • Protein or peptide: Phycocyanin beta chain
    • Protein or peptide: Phycocyanin alpha chain
    • Protein or peptide: Phycocyanin-associated rod linker protein
    • Protein or peptide: Glr1262 protein
  • Ligand: PHYCOCYANOBILIN

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Supramolecule #1: Bundle-shaped phycobilisome

SupramoleculeName: Bundle-shaped phycobilisome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)

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Macromolecule #1: Phycocyanin-associated rod linker protein

MacromoleculeName: Phycocyanin-associated rod linker protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 31.085066 KDa
SequenceString: MSVLTGDNQQ RGSKLFKITI ALSPTLAHHP WPGLDTHEPS QSSYSTIVSL ERLLPEMTRI KRNGGRILEI TEGEASESRA NFPAVMEPP VVELYPRAGE AEVQAVIAVA YKQVFGNIHV MESERIVSAE SLLRNRSISV REFVRLLAKS DLYKESFFHC T SNNRFIEL ...String:
MSVLTGDNQQ RGSKLFKITI ALSPTLAHHP WPGLDTHEPS QSSYSTIVSL ERLLPEMTRI KRNGGRILEI TEGEASESRA NFPAVMEPP VVELYPRAGE AEVQAVIAVA YKQVFGNIHV MESERIVSAE SLLRNRSISV REFVRLLAKS DLYKESFFHC T SNNRFIEL NFKHLLGRAP YNHSEIIEHL DRYQSQGYDA EIDSYIDSDE YVKTFGENVV PYHRGFKSQV GQQSVAAFER MI RLFGGDA SSDTSLNRTG QKRLVDPKQL LRSGRGIV

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Macromolecule #2: Phycocyanin beta chain

MacromoleculeName: Phycocyanin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 18.478953 KDa
SequenceString:
MQDAFTKAIV AADLRGSFLS EQELNQLTNL VKESNKRLDA VNAITGNAAE IISDAAHKLF AEQTDLIRPG GNAYPNRRMA ACLRDMEII LRYVSYALLA GDASVLEDRC LNGLKETYVA LGTPTRSVAR AVQLMKETAI GYVNSPSGVT RGDCSALVNE A ATYFDKAA ASIA

UniProtKB: Phycocyanin beta chain

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Macromolecule #3: Phycocyanin alpha chain

MacromoleculeName: Phycocyanin alpha chain / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 17.679852 KDa
SequenceString:
MKTVITEVIA SADSQGRFLN NTELQAANGR FQRATASMEA ARALTSNADS LVKGAVQEVY NKFPYLTQPG QMGYGDTNQA KCARDISHY LRFITYSLVA GGTGPLDDYI VAGLREVNRT FNLSPSWYIE ALKHIKGKVG SQLSGQPLTE ANAYIDYCIN A LS

UniProtKB: Phycocyanin alpha chain

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Macromolecule #4: Phycocyanin-associated rod linker protein

MacromoleculeName: Phycocyanin-associated rod linker protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 30.913822 KDa
SequenceString: MNVLTTSSQR GGKLFKVTMT LSPALSHHPW PSLDTYEPSQ NSYSVVVPLD RLLAEMTYIK NKGGRVLDIS PADLEALGPP DISSVAIPL KVELWAKADV SDVQAAIVAA YKQIFGNTYV LESERLTSAE SLLRNGSISV REFVRLLAKS ELYKERFFFC T SNNRFTEL ...String:
MNVLTTSSQR GGKLFKVTMT LSPALSHHPW PSLDTYEPSQ NSYSVVVPLD RLLAEMTYIK NKGGRVLDIS PADLEALGPP DISSVAIPL KVELWAKADV SDVQAAIVAA YKQIFGNTYV LESERLTSAE SLLRNGSISV REFVRLLAKS ELYKERFFFC T SNNRFTEL NFKHFLGRAP YNQSEIAAHL DRYQTFGYDA EIDSYIDSDE YIQAFGENVV PYYRGFKSQS GQTVESFNRM FK LYRGDAG SDTNLNLQGQ KRRVDPKNLL RSGRGIV

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Macromolecule #5: Glr1262 protein

MacromoleculeName: Glr1262 protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 92.127602 KDa
SequenceString: MSTVLDDQSK AYAPGSANGP TAGLEPFVRM SRMIRSGVPE DREEPDELWL SMVRDIFGRG YMDRLSQTRA IDYSAFVRPA DQATADGAA QTKLGITAIA PDQGVELRPN FTEADVITVI RAAYKQLFGN TYILESERVI QAESLLRNGS ISVREFIRIL A KSDLYKER ...String:
MSTVLDDQSK AYAPGSANGP TAGLEPFVRM SRMIRSGVPE DREEPDELWL SMVRDIFGRG YMDRLSQTRA IDYSAFVRPA DQATADGAA QTKLGITAIA PDQGVELRPN FTEADVITVI RAAYKQLFGN TYILESERVI QAESLLRNGS ISVREFIRIL A KSDLYKER FFRCTSNNRF IELNLKHLLG RAPYNQGEIA EHLDRYCQSG YDAEIDSYID SDEYRRVFGE NTVPYFRGFK YQ VGQSAAA FERMRALYSG DAGSDTDRNQ NGQRTELTSG LADPAQPVRA RTDYALTRVD IPGGNGAAGR LAALDESLGS WLD AARDLI SQNDYSQKAI EVEPKRVAPY AQYLTPAVEA TPDAAAQTKL GITAVAPDQA VELRPNFGEA EVQAVIRAAY KQIF GNTYI LEADRVVIAE SLLRNGSISV REFVRLLAKS DLYRDRFFRT ASNNRFIELN FKHFLGRAPY SQAEIGEHFN RYHKS GYDA EIDSYIDSDE YRRVFGENTV PYFRGFKYQV GQAARGFDQM QQLFAGDAGS DTDRGIGAQP AAKLTFPLSR PLGVTS AYF PSSQGGAATS DGLEMFTRMA RELTVTPVSA RRTTSPTAPT APAMPLAGYY SRPAPRATAD GDAQTKLGIT AVAPAQA VE LRPNFGETEL QAVIRATYKQ LFGNTYILEA DRVVQAESLL RNGSINVREF VRLLAKSELY KERFFHCTSN NRFIELTF K HLLGRAPYNQ SEFVEHLDRY QKSGYDAEID SYIDSDEYRR VFGENTVPYF RGFKYQTGQA AGVFERTLKL YGGDADSDT NRNRQGQLRQ VDPQELLRSG RGIV

UniProtKB: Glr1262 protein

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Macromolecule #6: PHYCOCYANOBILIN

MacromoleculeName: PHYCOCYANOBILIN / type: ligand / ID: 6 / Number of copies: 36 / Formula: CYC
Molecular weightTheoretical: 588.694 Da
Chemical component information

ChemComp-CYC:
PHYCOCYANOBILIN

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7 / Component - Concentration: 50.0 mM / Component - Formula: Tris-HCl
Component - Name: Tris(hydroxymethyl)aminomethane hydrochloride
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: Microscope was modified with a Cs corrector (CEOS GmbH, Germany).
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
DetailsPreliminary grid screening was performed manually.
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average exposure time: 3.9 sec. / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 85000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Warp (ver. 1.0.9) / Type: NONE
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 207644
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)

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